organise mastersheet
## Reading from 'FILTURB_datasheet'
## Range "'Master_Samplesheet'"
## Showing xtabs for entire datasheet, including Sample_Type by default
## , , Primer_set = 12SV5.2, study = Both
##
## experiment_id
## sample_type 2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
## Extraction_Negative 0 0 0 0 0
## Field 0 0 0 0 0
## Field_Negative 0 0 0 0 0
## PCR_negative 0 0 0 0 0
## Tissue 0 0 2 0 0
##
## , , Primer_set = 12SV51, study = Both
##
## experiment_id
## sample_type 2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
## Extraction_Negative 0 0 0 0 0
## Field 0 0 0 0 0
## Field_Negative 0 0 0 0 0
## PCR_negative 0 0 0 0 0
## Tissue 0 0 2 0 4
##
## , , Primer_set = LERAY-XT, study = Both
##
## experiment_id
## sample_type 2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
## Extraction_Negative 0 0 0 0 0
## Field 0 0 0 0 0
## Field_Negative 0 0 0 0 0
## PCR_negative 0 0 0 0 0
## Tissue 0 0 0 0 0
##
## , , Primer_set = 12SV5.2, study = North
##
## experiment_id
## sample_type 2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
## Extraction_Negative 0 2 0 0 0
## Field 0 23 0 0 0
## Field_Negative 0 0 0 0 0
## PCR_negative 0 0 1 0 0
## Tissue 0 0 0 0 0
##
## , , Primer_set = 12SV51, study = North
##
## experiment_id
## sample_type 2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
## Extraction_Negative 0 0 12 0 0
## Field 0 1 114 0 0
## Field_Negative 0 0 40 0 0
## PCR_negative 4 1 3 0 0
## Tissue 0 0 0 0 0
##
## , , Primer_set = LERAY-XT, study = North
##
## experiment_id
## sample_type 2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
## Extraction_Negative 0 0 0 0 0
## Field 0 0 0 72 0
## Field_Negative 0 0 0 0 0
## PCR_negative 0 0 0 0 0
## Tissue 0 0 0 0 0
##
## , , Primer_set = 12SV5.2, study = South
##
## experiment_id
## sample_type 2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
## Extraction_Negative 0 0 10 0 0
## Field 0 0 194 0 0
## Field_Negative 0 0 32 0 0
## PCR_negative 0 0 5 0 0
## Tissue 0 0 0 0 0
##
## , , Primer_set = 12SV51, study = South
##
## experiment_id
## sample_type 2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
## Extraction_Negative 0 0 10 0 0
## Field 0 0 194 0 0
## Field_Negative 0 0 32 0 0
## PCR_negative 0 0 4 0 0
## Tissue 0 0 0 0 0
##
## , , Primer_set = LERAY-XT, study = South
##
## experiment_id
## sample_type 2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
## Extraction_Negative 0 0 0 0 0
## Field 0 0 0 64 0
## Field_Negative 0 0 0 6 0
## PCR_negative 0 0 0 2 0
## Tissue 0 0 0 0 0
##
## , , Primer_set = 12SV5.2, study = Test
##
## experiment_id
## sample_type 2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
## Extraction_Negative 0 0 0 0 0
## Field 0 0 0 0 0
## Field_Negative 0 0 0 0 0
## PCR_negative 0 0 0 0 0
## Tissue 0 0 0 0 0
##
## , , Primer_set = 12SV51, study = Test
##
## experiment_id
## sample_type 2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
## Extraction_Negative 0 0 0 0 0
## Field 14 0 0 0 0
## Field_Negative 0 0 0 0 0
## PCR_negative 2 0 0 0 0
## Tissue 0 0 0 0 0
##
## , , Primer_set = LERAY-XT, study = Test
##
## experiment_id
## sample_type 2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
## Extraction_Negative 0 0 0 0 0
## Field 0 0 0 0 0
## Field_Negative 0 0 0 0 0
## PCR_negative 0 0 0 0 0
## Tissue 0 0 0 0 0
## Subsetting datasheet, check output to see if it made sense
## $experiment_id
## [1] "2018_07"
##
## $Primer_set
## [1] "12SV5.2"
##
## $study
## [1] "South"
## , , Primer_set = 12SV5.2, study = South
##
## experiment_id
## sample_type 2018_07
## Extraction_Negative 10
## Field 194
## Field_Negative 32
## PCR_negative 5
test removing contaminants blindly
## Based on Field_Negative FILTURB-F100-A-N4-12S2-2018_07 , Removing detections of
## [1] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;Alytes obstetricans"
## [2] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;NA"
## [3] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;NA;NA"
## from
## [1] "FILTURB-F95-A-N3-12S2-2018_07" "FILTURB-F96-A-N3-12S2-2018_07"
## [3] "FILTURB-F97-A-N3-12S2-2018_07" "FILTURB-F98-A-N3-12S2-2018_07"
## [5] "FILTURB-F99-A-N3-12S2-2018_07" "FILTURB-F100-A-N3-12S2-2018_07"
## [7] "FILTURB-C33-A-N3-12S2-2018_07" "FILTURB-F95-A-N4-12S2-2018_07"
## [9] "FILTURB-F96-A-N4-12S2-2018_07" "FILTURB-F97-A-N4-12S2-2018_07"
## [11] "FILTURB-F98-A-N4-12S2-2018_07" "FILTURB-F99-A-N4-12S2-2018_07"
## [13] "FILTURB-F100-A-N4-12S2-2018_07" "FILTURB-C33-A-N4-12S2-2018_07"
## which all belong to Site : B06a
## 12665 reads removed from 3 detection(s) in 1 sample(s), of which 12665 were in the negative. See table below for details:
## Not printing contamination table
## Based on Field_Negative FILTURB-F106-A-N4-12S2-2018_07 , Removing detections of
## [1] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;Alytes obstetricans"
## [2] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;NA"
## from
## [1] "FILTURB-F101-A-N3-12S2-2018_07" "FILTURB-F103-A-N3-12S2-2018_07"
## [3] "FILTURB-F104-A-N3-12S2-2018_07" "FILTURB-F106-A-N3-12S2-2018_07"
## [5] "FILTURB-C34-A-N3-12S2-2018_07" "FILTURB-F102-A-N3-12S2-2018_07"
## [7] "FILTURB-F105-A-N3-12S2-2018_07" "FILTURB-F101-A-N4-12S2-2018_07"
## [9] "FILTURB-F103-A-N4-12S2-2018_07" "FILTURB-F104-A-N4-12S2-2018_07"
## [11] "FILTURB-F106-A-N4-12S2-2018_07" "FILTURB-C34-A-N4-12S2-2018_07"
## [13] "FILTURB-F102-A-N4-12S2-2018_07" "FILTURB-F105-A-N4-12S2-2018_07"
## which all belong to Site : B20a
## 3905 reads removed from 2 detection(s) in 1 sample(s), of which 3905 were in the negative. See table below for details:
## Not printing contamination table
## Based on Field_Negative FILTURB-F125-A-N3-12S2-2018_07 , Removing detections of
## [1] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;Alytes obstetricans"
## [2] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;NA"
## [3] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Lissotriton;NA"
## [4] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;NA;NA"
## [5] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Pleurodeles;NA"
## [6] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Pleurodeles;Pleurodeles waltl"
## from
## [1] "FILTURB-F119-A-N3-12S2-2018_07" "FILTURB-F120-A-N3-12S2-2018_07"
## [3] "FILTURB-F121-A-N3-12S2-2018_07" "FILTURB-F122-A-N3-12S2-2018_07"
## [5] "FILTURB-F123-A-N3-12S2-2018_07" "FILTURB-C37-A-N3-12S2-2018_07"
## [7] "FILTURB-F125-A-N3-12S2-2018_07" "FILTURB-F124-A-N3-12S2-2018_07"
## [9] "FILTURB-F119-A-N4-12S2-2018_07" "FILTURB-F120-A-N4-12S2-2018_07"
## [11] "FILTURB-F121-A-N4-12S2-2018_07" "FILTURB-F122-A-N4-12S2-2018_07"
## [13] "FILTURB-F123-A-N4-12S2-2018_07" "FILTURB-C37-A-N4-12S2-2018_07"
## [15] "FILTURB-F125-A-N4-12S2-2018_07" "FILTURB-F124-A-N4-12S2-2018_07"
## which all belong to Site : A01
## 9393 reads removed from 24 detection(s) in 7 sample(s), of which 3196 were in the negative. See table below for details:
## Not printing contamination table
## Based on Field_Negative FILTURB-F125-A-N4-12S2-2018_07 , Removing detections of
## [1] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;Alytes obstetricans"
## [2] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;NA"
## [3] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Discoglossus;NA"
## [4] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;NA;NA"
## [5] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;Hyla meridionalis"
## [6] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;NA"
## [7] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;NA;NA"
## [8] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Salamandra;NA"
## [9] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Salamandra;Salamandra salamandra"
## [10] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Triturus;NA"
## [11] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Triturus;Triturus marmoratus"
## [12] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Triturus;Triturus pygmaeus"
## [13] "Eukaryota;Chordata;Amphibia;unknown;NA;NA;NA"
## from
## [1] "FILTURB-F119-A-N3-12S2-2018_07" "FILTURB-F120-A-N3-12S2-2018_07"
## [3] "FILTURB-F121-A-N3-12S2-2018_07" "FILTURB-F122-A-N3-12S2-2018_07"
## [5] "FILTURB-F123-A-N3-12S2-2018_07" "FILTURB-C37-A-N3-12S2-2018_07"
## [7] "FILTURB-F125-A-N3-12S2-2018_07" "FILTURB-F124-A-N3-12S2-2018_07"
## [9] "FILTURB-F119-A-N4-12S2-2018_07" "FILTURB-F120-A-N4-12S2-2018_07"
## [11] "FILTURB-F121-A-N4-12S2-2018_07" "FILTURB-F122-A-N4-12S2-2018_07"
## [13] "FILTURB-F123-A-N4-12S2-2018_07" "FILTURB-C37-A-N4-12S2-2018_07"
## [15] "FILTURB-F125-A-N4-12S2-2018_07" "FILTURB-F124-A-N4-12S2-2018_07"
## which all belong to Site : A01
## 24066 reads removed from 27 detection(s) in 8 sample(s), of which 8826 were in the negative. See table below for details:
## Not printing contamination table
## Based on Field_Negative FILTURB-F34-A-N3-12S2-2018_07 , Removing detections of
## [1] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;NA;NA"
## [2] "Eukaryota;Chordata;Amphibia;Anura;NA;NA;NA"
## from
## [1] "FILTURB-F29-A-N3-12S2-2018_07" "FILTURB-F30-A-N3-12S2-2018_07"
## [3] "FILTURB-F31-A-N3-12S2-2018_07" "FILTURB-F32-A-N3-12S2-2018_07"
## [5] "FILTURB-F33-A-N3-12S2-2018_07" "FILTURB-F34-A-N3-12S2-2018_07"
## [7] "FILTURB-C22-A-N3-12S2-2018_07" "FILTURB-F29-A-N4-12S2-2018_07"
## [9] "FILTURB-F30-A-N4-12S2-2018_07" "FILTURB-F31-A-N4-12S2-2018_07"
## [11] "FILTURB-F32-A-N4-12S2-2018_07" "FILTURB-F33-A-N4-12S2-2018_07"
## [13] "FILTURB-F34-A-N4-12S2-2018_07" "FILTURB-C22-A-N4-12S2-2018_07"
## which all belong to Site : G21
## 3990 reads removed from 7 detection(s) in 6 sample(s), of which 3756 were in the negative. See table below for details:
## Not printing contamination table
## Based on Field_Negative FILTURB-F40-A-N4-12S2-2018_07 , Removing detections of
## [1] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;Hyla meridionalis"
## [2] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;NA"
## from
## [1] "FILTURB-F35-A-N3-12S2-2018_07" "FILTURB-F36-A-N3-12S2-2018_07"
## [3] "FILTURB-F37-A-N3-12S2-2018_07" "FILTURB-F38-A-N3-12S2-2018_07"
## [5] "FILTURB-F39-A-N3-12S2-2018_07" "FILTURB-F40-A-N3-12S2-2018_07"
## [7] "FILTURB-C23-A-N3-12S2-2018_07" "FILTURB-F35-A-N4-12S2-2018_07"
## [9] "FILTURB-F36-A-N4-12S2-2018_07" "FILTURB-F37-A-N4-12S2-2018_07"
## [11] "FILTURB-F38-A-N4-12S2-2018_07" "FILTURB-F39-A-N4-12S2-2018_07"
## [13] "FILTURB-F40-A-N4-12S2-2018_07" "FILTURB-C23-A-N4-12S2-2018_07"
## which all belong to Site : G35
## 70665 reads removed from 21 detection(s) in 12 sample(s), of which 4445 were in the negative. See table below for details:
## Not printing contamination table
## Based on Field_Negative FILTURB-F46-A-N4-12S2-2018_07 , Removing detections of
## [1] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;Alytes obstetricans"
## [2] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;NA"
## [3] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;NA;NA"
## [4] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;Hyla meridionalis"
## [5] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;NA"
## [6] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;NA;NA"
## from
## [1] "FILTURB-F41-A-N3-12S2-2018_07" "FILTURB-F42-A-N3-12S2-2018_07"
## [3] "FILTURB-F43-A-N3-12S2-2018_07" "FILTURB-F44-A-N3-12S2-2018_07"
## [5] "FILTURB-F45-A-N3-12S2-2018_07" "FILTURB-F46-A-N3-12S2-2018_07"
## [7] "FILTURB-C24-A-N3-12S2-2018_07" "FILTURB-F41-A-N4-12S2-2018_07"
## [9] "FILTURB-F42-A-N4-12S2-2018_07" "FILTURB-F43-A-N4-12S2-2018_07"
## [11] "FILTURB-F44-A-N4-12S2-2018_07" "FILTURB-F45-A-N4-12S2-2018_07"
## [13] "FILTURB-F46-A-N4-12S2-2018_07" "FILTURB-C24-A-N4-12S2-2018_07"
## which all belong to Site : G16
## 76062 reads removed from 29 detection(s) in 9 sample(s), of which 12151 were in the negative. See table below for details:
## Not printing contamination table
## Based on Field_Negative FILTURB-F52-A-N3-12S2-2018_07 , Removing detections of
## [1] "Eukaryota;Chordata;Amphibia;Anura;NA;NA;NA"
## from
## [1] "FILTURB-F47-A-N3-12S2-2018_07" "FILTURB-F48-A-N3-12S2-2018_07"
## [3] "FILTURB-F49-A-N3-12S2-2018_07" "FILTURB-F50-A-N3-12S2-2018_07"
## [5] "FILTURB-F51-A-N3-12S2-2018_07" "FILTURB-F52-A-N3-12S2-2018_07"
## [7] "FILTURB-C25-A-N3-12S2-2018_07" "FILTURB-F47-A-N4-12S2-2018_07"
## [9] "FILTURB-F49-A-N4-12S2-2018_07" "FILTURB-F50-A-N4-12S2-2018_07"
## [11] "FILTURB-F51-A-N4-12S2-2018_07" "FILTURB-F52-A-N4-12S2-2018_07"
## [13] "FILTURB-C25-A-N4-12S2-2018_07" "FILTURB-F48-A-N4-12S2-2018_07"
## which all belong to Site : G09
## 5347 reads removed from 1 detection(s) in 1 sample(s), of which 5347 were in the negative. See table below for details:
## Not printing contamination table
## Based on Field_Negative FILTURB-F64-A-N3-12S2-2018_07 , Removing detections of
## [1] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;Hyla meridionalis"
## [2] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;NA"
## from
## [1] "FILTURB-F59-A-N3-12S2-2018_07" "FILTURB-F60-A-N3-12S2-2018_07"
## [3] "FILTURB-F61-A-N3-12S2-2018_07" "FILTURB-F62-A-N3-12S2-2018_07"
## [5] "FILTURB-F64-A-N3-12S2-2018_07" "FILTURB-F63-A-N3-12S2-2018_07"
## [7] "FILTURB-C27-A-N3-12S2-2018_07" "FILTURB-F59-A-N4-12S2-2018_07"
## [9] "FILTURB-F60-A-N4-12S2-2018_07" "FILTURB-F61-A-N4-12S2-2018_07"
## [11] "FILTURB-F62-A-N4-12S2-2018_07" "FILTURB-F64-A-N4-12S2-2018_07"
## [13] "FILTURB-F63-A-N4-12S2-2018_07" "FILTURB-C27-A-N4-12S2-2018_07"
## which all belong to Site : G60
## 28665 reads removed from 11 detection(s) in 6 sample(s), of which 9554 were in the negative. See table below for details:
## Not printing contamination table
## Based on Field_Negative FILTURB-F64-A-N4-12S2-2018_07 , Removing detections of
## [1] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;Hyla meridionalis"
## [2] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;NA"
## [3] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;NA;NA"
## from
## [1] "FILTURB-F59-A-N3-12S2-2018_07" "FILTURB-F60-A-N3-12S2-2018_07"
## [3] "FILTURB-F61-A-N3-12S2-2018_07" "FILTURB-F62-A-N3-12S2-2018_07"
## [5] "FILTURB-F64-A-N3-12S2-2018_07" "FILTURB-F63-A-N3-12S2-2018_07"
## [7] "FILTURB-C27-A-N3-12S2-2018_07" "FILTURB-F59-A-N4-12S2-2018_07"
## [9] "FILTURB-F60-A-N4-12S2-2018_07" "FILTURB-F61-A-N4-12S2-2018_07"
## [11] "FILTURB-F62-A-N4-12S2-2018_07" "FILTURB-F64-A-N4-12S2-2018_07"
## [13] "FILTURB-F63-A-N4-12S2-2018_07" "FILTURB-C27-A-N4-12S2-2018_07"
## which all belong to Site : G60
## 1528 reads removed from 3 detection(s) in 3 sample(s), of which 6786 were in the negative. See table below for details:
## Not printing contamination table
## Based on Field_Negative FILTURB-F76-A-N4-12S2-2018_07 , Removing detections of
## [1] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Lissotriton;Lissotriton helveticus"
## [2] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Lissotriton;NA"
## [3] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;NA;NA"
## from
## [1] "FILTURB-F71-A-N3-12S2-2018_07" "FILTURB-F73-A-N3-12S2-2018_07"
## [3] "FILTURB-F74-A-N3-12S2-2018_07" "FILTURB-F75-A-N3-12S2-2018_07"
## [5] "FILTURB-F76-A-N3-12S2-2018_07" "FILTURB-C29-A-N3-12S2-2018_07"
## [7] "FILTURB-F72-A-N3-12S2-2018_07" "FILTURB-F71-A-N4-12S2-2018_07"
## [9] "FILTURB-F73-A-N4-12S2-2018_07" "FILTURB-F74-A-N4-12S2-2018_07"
## [11] "FILTURB-F75-A-N4-12S2-2018_07" "FILTURB-F76-A-N4-12S2-2018_07"
## [13] "FILTURB-C29-A-N4-12S2-2018_07" "FILTURB-F72-A-N4-12S2-2018_07"
## which all belong to Site : VB01
## 6918 reads removed from 4 detection(s) in 2 sample(s), of which 6650 were in the negative. See table below for details:
## Not printing contamination table
## Based on Field_Negative FILTURB-F94-A-N3-12S2-2018_07 , Removing detections of
## [1] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;NA;NA"
## [2] "Eukaryota;Chordata;Amphibia;Anura;NA;NA;NA"
## from
## [1] "FILTURB-F89-A-N3-12S2-2018_07" "FILTURB-F90-A-N3-12S2-2018_07"
## [3] "FILTURB-F93-A-N3-12S2-2018_07" "FILTURB-F94-A-N3-12S2-2018_07"
## [5] "FILTURB-C32-A-N3-12S2-2018_07" "FILTURB-F91-A-N3-12S2-2018_07"
## [7] "FILTURB-F89-A-N4-12S2-2018_07" "FILTURB-F90-A-N4-12S2-2018_07"
## [9] "FILTURB-F93-A-N4-12S2-2018_07" "FILTURB-F94-A-N4-12S2-2018_07"
## [11] "FILTURB-C32-A-N4-12S2-2018_07" "FILTURB-F91-A-N4-12S2-2018_07"
## [13] "FILTURB-F92-A-N3-12S2-2018_07" "FILTURB-F92-A-N4-12S2-2018_07"
## which all belong to Site : 206b
## 9947 reads removed from 2 detection(s) in 1 sample(s), of which 9947 were in the negative. See table below for details:
## Not printing contamination table
## Based on Extraction_Negative FILTURB-EXTN_B10-A-N3-12S2-2018_07 , Removing detections of
## [1] "Eukaryota;Chordata;Amphibia;Anura;Pelobatidae;Pelobates;Pelobates cultripes"
## from
## character(0)
## which all belong to Site : NA
## 0 reads removed from 0 detection(s) in 0 sample(s), of which 1433 were in the negative. See table below for details:
## Not printing contamination table
## ***********A total of 253151 reads removed